{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T15:50:33Z","timestamp":1783093833075,"version":"3.54.6"},"reference-count":38,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2016,1,14]],"date-time":"2016-01-14T00:00:00Z","timestamp":1452729600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2016,1,14]],"date-time":"2016-01-14T00:00:00Z","timestamp":1452729600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>To determine the origin and evolutionary history of two predominant and closely-related circulating recombinant forms (CRF07_BC and CRF08_BC), recombinant structures and phylogenies of 7 unique recombinant forms comprised of subtypes of B\u2019 (Thai B linage) and C (designated URFs_BC) from archival specimens of injection drug users (IDUs) collected in 1996 to 1998 from western Yunnan and 4 circulating recombinant forms with B\u2019\/C recombinants recently identified (designated nCRFs_BC) in China were compared with those of CRF07_BC and CRF08_BC. The results showed that 5 of 7 URFs_BC and all the nCRFs_BC shared recombination breakpoints with CRF07_BC and\/or CRF08_BC. Yunnan URFs_BC consistently occupied the basal branch positions compared with CRF07_BC, CRF08_BC and nCRFs_BC in phylogenetic trees. The estimated most recent common ancestors (tMRCA) for Yunnan URFs_BC were from ~1987, approximately half a decade earlier than those for CRF07_BC (~1994) and CRF08_BC (~1992). Discrete phylogeographic and spatial diffusion analysis revealed that both CRF07_BC and CRF08 BC came from western Yunnan in the early 1990s. Our results provide compelling evidence for western Yunnan as the geographic origin of CRF07_BC and CRF08_BC, which emerged from a swarm of URFs_BC by a series of recombination events in western Yunnan in the early 1990s.<\/jats:p>","DOI":"10.1038\/srep19279","type":"journal-article","created":{"date-parts":[[2016,1,14]],"date-time":"2016-01-14T14:15:04Z","timestamp":1452780904000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":90,"title":["Geographic origin and evolutionary history of China\u2019s two predominant HIV-1 circulating recombinant forms, CRF07_BC and CRF08_BC"],"prefix":"10.1038","volume":"6","author":[{"given":"Yi","family":"Feng","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yutaka","family":"Takebe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huamian","family":"Wei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiang","family":"He","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jenny H.","family":"Hsi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhenpeng","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hui","family":"Xing","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuhua","family":"Ruan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yao","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fan","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Wei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xingguang","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yiming","family":"Shao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2016,1,14]]},"reference":[{"key":"BFsrep19279_CR1","first-page":"235","volume":"4","author":"SL Qin","year":"1989","unstructured":"Qin, S. L. et al. First case of sexual transmission of human immunodeficiency virus in mainland China. Proceedings of the Chinese Academy of Medical Sciences and the Peking Union Medical College = Chung-kuo i hsueh k\u2019o hsueh yuan, Chung-kuo hsieh ho i k\u2019o ta hsueh hsueh pao 4, 235\u2013236 (1989).","journal-title":"Proceedings of the Chinese Academy of Medical Sciences and the Peking Union Medical College = Chung-kuo i hsueh k\u2019o hsueh yuan, Chung-kuo hsieh ho i k\u2019o ta hsueh hsueh pao"},{"key":"BFsrep19279_CR2","first-page":"646","volume":"71","author":"N Wang","year":"1991","unstructured":"Wang, N. [First reported case of AIDS in China]. Zhonghua yi xue za zhi 71, 671\u2013673, 646 (1991).","journal-title":"Zhonghua yi xue za zhi"},{"key":"BFsrep19279_CR3","doi-asserted-by":"publisher","first-page":"e47289","DOI":"10.1371\/journal.pone.0047289","volume":"7","author":"X He","year":"2012","unstructured":"He, X. et al. A comprehensive mapping of HIV-1 genotypes in various risk groups and regions across China based on a nationwide molecular epidemiologic survey. PLoS One 7, e47289, 10.1371\/journal.pone.0047289 (2012).","journal-title":"PLoS One"},{"key":"BFsrep19279_CR4","doi-asserted-by":"publisher","first-page":"877","DOI":"10.1097\/QAD.0b013e328351430d","volume":"26","author":"Z Li","year":"2012","unstructured":"Li, Z. et al. Tracing the origin and history of HIV-1 subtype B\u2019 epidemic by near full-length genome analyses. AIDS 26, 877\u2013884, 10.1097\/QAD.0b013e328351430d (2012).","journal-title":"AIDS"},{"key":"BFsrep19279_CR5","doi-asserted-by":"publisher","first-page":"B39","DOI":"10.1016\/j.vaccine.2009.07.101","volume":"28","author":"Y Takebe","year":"2010","unstructured":"Takebe, Y. et al. Reconstructing the epidemic history of HIV-1 circulating recombinant forms CRF07_BC and CRF08_BC in East Asia: the relevance of genetic diversity and phylodynamics for vaccine strategies. Vaccine 28 Suppl 2, B39\u201344, 10.1016\/j.vaccine.2009.07.101 (2010).","journal-title":"Vaccine"},{"key":"BFsrep19279_CR6","doi-asserted-by":"publisher","first-page":"9206","DOI":"10.1128\/JVI.00399-08","volume":"82","author":"KK Tee","year":"2008","unstructured":"Tee, K. K. et al. Temporal and spatial dynamics of human immunodeficiency virus type 1 circulating recombinant forms 08_BC and 07_BC in Asia. J Virol 82, 9206\u20139215, 10.1128\/JVI.00399-08 (2008).","journal-title":"J Virol"},{"key":"BFsrep19279_CR7","doi-asserted-by":"publisher","first-page":"1135","DOI":"10.1089\/088922202320567879","volume":"18","author":"FE McClutchan","year":"2002","unstructured":"McClutchan, F. E. et al. Precise mapping of recombination breakpoints suggests a common parent of two BC recombinant HIV type 1 strains circulating in China. AIDS Res Hum Retroviruses 18, 1135\u20131140, 10.1089\/088922202320567879 (2002).","journal-title":"AIDS Res Hum Retroviruses"},{"key":"BFsrep19279_CR8","first-page":"129","volume":"12","author":"Y Shao","year":"1991","unstructured":"Shao, Y. et al. Isolation of viruses from HIV infected individuals in Yunnan. Chin J Epidemiol 12, 129 (1991).","journal-title":"Chin J Epidemiol"},{"key":"BFsrep19279_CR9","doi-asserted-by":"publisher","first-page":"1051","DOI":"10.1089\/aid.2005.21.1051","volume":"21","author":"Z Qiu","year":"2005","unstructured":"Qiu, Z. et al. Characterization of five nearly full-length genomes of early HIV type 1 strains in Ruili city: implications for the genesis of CRF07_BC and CRF08_BC circulating in China. AIDS Res Hum Retroviruses 21, 1051\u20131056, 10.1089\/aid.2005.21.1051 (2005).","journal-title":"AIDS Res Hum Retroviruses"},{"key":"BFsrep19279_CR10","doi-asserted-by":"publisher","first-page":"1141","DOI":"10.1097\/00002030-199408000-00017","volume":"8","author":"X Zheng","year":"1994","unstructured":"Zheng, X. et al. Injecting drug use and HIV infection in southwest China. AIDS 8, 1141\u20131147 (1994).","journal-title":"AIDS"},{"key":"BFsrep19279_CR11","doi-asserted-by":"publisher","first-page":"e52373","DOI":"10.1371\/journal.pone.0052373","volume":"7","author":"Z Meng","year":"2012","unstructured":"Meng, Z. et al. A new migration map of HIV-1 CRF07_BC in China: analysis of sequences from 12 provinces over a decade. PLoS One 7, e52373, 10.1371\/journal.pone.0052373 (2012).","journal-title":"PLoS One"},{"key":"BFsrep19279_CR12","doi-asserted-by":"publisher","first-page":"e23347","DOI":"10.1371\/journal.pone.0023347","volume":"6","author":"J Liu","year":"2011","unstructured":"Liu, J. & Zhang, C. Phylogeographic analyses reveal a crucial role of Xinjiang in HIV-1 CRF07_BC and HCV 3a transmissions in Asia. PLoS One 6, e23347, 10.1371\/journal.pone.0023347 (2011).","journal-title":"PLoS One"},{"key":"BFsrep19279_CR13","first-page":"184","volume":"11","author":"Y Ma","year":"1990","unstructured":"Ma, Y., Li, Z. & Zhang, K. HIV was first discovered among injecting drug users in China. Chin J Epidemiol 11(3), 184 (1990).","journal-title":"Chin J Epidemiol"},{"key":"BFsrep19279_CR14","doi-asserted-by":"publisher","first-page":"1171","DOI":"10.1016\/0140-6736(93)91001-3","volume":"341","author":"CY Ou","year":"1993","unstructured":"Ou, C. Y. et al. Independent introduction of two major HIV-1 genotypes into distinct high-risk populations in Thailand. Lancet 341, 1171\u20131174 (1993).","journal-title":"Lancet"},{"key":"BFsrep19279_CR15","doi-asserted-by":"publisher","first-page":"S13","DOI":"10.1097\/00002030-199407000-00020","volume":"8","author":"BG Weniger","year":"1994","unstructured":"Weniger, B. G., Takebe, Y., Ou, C. Y. & Yamazaki, S. The molecular epidemiology of HIV in Asia. AIDS 8 Suppl 2, S13\u201328 (1994).","journal-title":"AIDS"},{"key":"BFsrep19279_CR16","doi-asserted-by":"publisher","first-page":"851","DOI":"10.1097\/00002030-199508000-00004","volume":"9","author":"ML Kalish","year":"1995","unstructured":"Kalish, M. L. et al. The evolving molecular epidemiology of HIV-1 envelope subtypes in injecting drug users in Bangkok, Thailand: implications for HIV vaccine trials. AIDS 9, 851\u2013857 (1995).","journal-title":"AIDS"},{"key":"BFsrep19279_CR17","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1097\/00002030-200001070-00009","volume":"14","author":"C Beyrer","year":"2000","unstructured":"Beyrer, C. et al. Overland heroin trafficking routes and HIV-1 spread in south and south-east Asia. AIDS 14, 75\u201383 (2000).","journal-title":"AIDS"},{"key":"BFsrep19279_CR18","doi-asserted-by":"publisher","first-page":"223","DOI":"10.1016\/j.virol.2010.03.048","volume":"402","author":"Y Li","year":"2010","unstructured":"Li, Y. et al. Explosive HIV-1 subtype B\u2019 epidemics in Asia driven by geographic and risk group founder events. Virology 402, 223\u2013227, 10.1016\/j.virol.2010.03.048 (2010).","journal-title":"Virology"},{"key":"BFsrep19279_CR19","doi-asserted-by":"publisher","first-page":"1051","DOI":"10.1016\/S0140-6736(95)90792-0","volume":"345","author":"CC Luo","year":"1995","unstructured":"Luo, C. C. et al. HIV-1 subtype C in China. Lancet 345, 1051\u20131052 (1995).","journal-title":"Lancet"},{"key":"BFsrep19279_CR20","first-page":"9","volume":"12","author":"Y Shao","year":"1996","unstructured":"Shao, Y. et al. Genetic variations and molecular epidemiology of the Ruili HIV-1 strains of Yunnan 1n 1995. Chin J Virol 12, 9 (1996).","journal-title":"Chin J Virol"},{"key":"BFsrep19279_CR21","doi-asserted-by":"publisher","first-page":"e25956","DOI":"10.1371\/journal.pone.0025956","volume":"6","author":"C Shen","year":"2011","unstructured":"Shen, C., Craigo, J., Ding, M., Chen, Y. & Gupta, P. Origin and dynamics of HIV-1 subtype C infection in India. PLoS One 6, e25956, 10.1371\/journal.pone.0025956 (2011).","journal-title":"PLoS One"},{"key":"BFsrep19279_CR22","doi-asserted-by":"publisher","first-page":"e39819","DOI":"10.1371\/journal.pone.0039819","volume":"7","author":"U Neogi","year":"2012","unstructured":"Neogi, U. et al. Molecular epidemiology of HIV-1 subtypes in India: origin and evolutionary history of the predominant subtype C. PLoS One 7, e39819, 10.1371\/journal.pone.0039819 (2012).","journal-title":"PLoS One"},{"key":"BFsrep19279_CR23","first-page":"109","volume":"13","author":"Y Shao","year":"1999","unstructured":"Shao, Y., Zhao, F., Yang, W., Zhang, Y. & Gong, X. The identification of recombinant HIV-1 strains in IDUs in southwest and northwest China. Chinese J Exp Clin Virol 13, 109 (1999).","journal-title":"Chinese J Exp Clin Virol"},{"key":"BFsrep19279_CR24","doi-asserted-by":"publisher","first-page":"11367","DOI":"10.1128\/JVI.74.23.11367-11376.2000","volume":"74","author":"L Su","year":"2000","unstructured":"Su, L. et al. Characterization of a virtually full-length human immunodeficiency virus type 1 genome of a prevalent intersubtype (C\/B\u2019) recombinant strain in China. J Virol 74, 11367\u201311376 (2000).","journal-title":"J Virol"},{"key":"BFsrep19279_CR25","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1089\/08892220150217247","volume":"17","author":"CM Rodenburg","year":"2001","unstructured":"Rodenburg, C. M. et al. Near full-length clones and reference sequences for subtype C isolates of HIV type 1 from three different continents. AIDS Res Hum Retroviruses 17, 161\u2013168, 10.1089\/08892220150217247 (2001).","journal-title":"AIDS Res Hum Retroviruses"},{"key":"BFsrep19279_CR26","doi-asserted-by":"publisher","first-page":"11286","DOI":"10.1128\/JVI.74.23.11286-11295.2000","volume":"74","author":"S Piyasirisilp","year":"2000","unstructured":"Piyasirisilp, S. et al. A recent outbreak of human immunodeficiency virus type 1 infection in southern China was initiated by two highly homogeneous, geographically separated strains, circulating recombinant form AE and a novel BC recombinant. J Virol 74, 11286\u201311295 (2000).","journal-title":"J Virol"},{"key":"BFsrep19279_CR27","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1128\/JVI.73.1.152-160.1999","volume":"73","author":"KS Lole","year":"1999","unstructured":"Lole, K. S. et al. Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol 73, 152\u2013160 (1999).","journal-title":"J Virol"},{"key":"BFsrep19279_CR28","doi-asserted-by":"publisher","first-page":"733","DOI":"10.1089\/aid.2007.0269","volume":"24","author":"L Bao","year":"2008","unstructured":"Bao, L. et al. Molecular tracing of sexual HIV Type 1 transmission in the southwest border of China. AIDS Res Hum Retroviruses 24, 733\u2013742, 10.1089\/aid.2007.0269 (2008).","journal-title":"AIDS Res Hum Retroviruses"},{"key":"BFsrep19279_CR29","doi-asserted-by":"crossref","unstructured":"Beyrer, C. The Golden Crescent and HIV\/AIDS in Central Asia: Deadly interactions. Glob Public Health, 1\u20137, 10.1080\/17441692.2011.572080 (2011).","DOI":"10.1080\/17441692.2011.572080"},{"key":"BFsrep19279_CR30","doi-asserted-by":"publisher","first-page":"11323","DOI":"10.1038\/srep11323","volume":"5","author":"H Wei","year":"2015","unstructured":"Wei, H. et al. The sexually driven epidemic in youths in China\u2019s southwestern border region was caused by dynamic emerging multiple recombinant HIV-1 strains. Scientific reports 5, 11323, 10.1038\/srep11323 (2015).","journal-title":"Scientific reports"},{"key":"BFsrep19279_CR31","doi-asserted-by":"publisher","first-page":"2212","DOI":"10.1128\/JVI.06184-11","volume":"86","author":"J Raghwani","year":"2012","unstructured":"Raghwani, J. et al. Origin and evolution of the unique hepatitis C virus circulating recombinant form 2k\/1b. J Virol 86, 2212\u20132220, 10.1128\/JVI.06184-11 (2012).","journal-title":"J Virol"},{"key":"BFsrep19279_CR32","doi-asserted-by":"publisher","first-page":"118","DOI":"10.1016\/j.jviromet.2006.04.009","volume":"136","author":"CM Rousseau","year":"2006","unstructured":"Rousseau, C. M. et al. Large-scale amplification, cloning and sequencing of near full-length HIV-1 subtype C genomes. J Virol Methods 136, 118\u2013125, 10.1016\/j.jviromet.2006.04.009 (2006).","journal-title":"J Virol Methods"},{"key":"BFsrep19279_CR33","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"25","author":"SF Altschul","year":"1997","unstructured":"Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25, 3389\u20133402 (1997).","journal-title":"Nucleic Acids Res"},{"key":"BFsrep19279_CR34","first-page":"95","volume":"41","author":"TA Hall","year":"1999","unstructured":"Hall, T. A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95\/98\/NT. Nucleic Acids Symp Ser 41, 95\u201398 (1999).","journal-title":"Nucleic Acids Symp Ser"},{"key":"BFsrep19279_CR35","doi-asserted-by":"publisher","first-page":"W463","DOI":"10.1093\/nar\/gkl255","volume":"34","author":"M Zhang","year":"2006","unstructured":"Zhang, M. et al. jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1. Nucleic Acids Res 34, W463\u2013465, 10.1093\/nar\/gkl255 (2006).","journal-title":"Nucleic Acids Res"},{"key":"BFsrep19279_CR36","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1186\/1471-2148-7-214","volume":"7","author":"AJ Drummond","year":"2007","unstructured":"Drummond, A. J. & Rambaut, A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7, 214, 10.1186\/1471-2148-7-214 (2007).","journal-title":"BMC Evol Biol"},{"key":"BFsrep19279_CR37","doi-asserted-by":"publisher","first-page":"e1000520","DOI":"10.1371\/journal.pcbi.1000520","volume":"5","author":"P Lemey","year":"2009","unstructured":"Lemey, P., Rambaut, A., Drummond, A. J. & Suchard, M. A. Bayesian phylogeography finds its roots. PLoS computational biology 5, e1000520, 10.1371\/journal.pcbi.1000520 (2009).","journal-title":"PLoS computational biology"},{"key":"BFsrep19279_CR38","doi-asserted-by":"publisher","first-page":"2910","DOI":"10.1093\/bioinformatics\/btr481","volume":"27","author":"F Bielejec","year":"2011","unstructured":"Bielejec, F., Rambaut, A., Suchard, M. A. & Lemey, P. SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics. Bioinformatics 27, 2910\u20132912, 10.1093\/bioinformatics\/btr481 (2011).","journal-title":"Bioinformatics"}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/srep19279.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/srep19279","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/srep19279.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,5]],"date-time":"2023-01-05T06:58:02Z","timestamp":1672901882000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/srep19279"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,1,14]]},"references-count":38,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2016,5,10]]}},"alternative-id":["BFsrep19279"],"URL":"https:\/\/doi.org\/10.1038\/srep19279","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,1,14]]},"assertion":[{"value":"28 October 2014","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 December 2015","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 January 2016","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing financial interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"19279"}}